Compositional constraint is the key force in shaping codon usage bias in hemagglutinin gene in H1N1 subtype of influenza a virus

International Journal of Genomics

Volumn 2014, Issue , 2014, Pages

  Deka, Himangshu ^a   Chakraborty, Supriyo ^a  

^a ASSAM UNIVERSITY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; INFLUENZA VIRUS HEMAGGLUTININ;

ARTICLE; CODING; CODON USAGE; CONTROLLED STUDY; FORCE; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; INFLUENZA VIRUS A H1N1; MOLECULAR PHYLOGENY; NONHUMAN; PRIORITY JOURNAL; RANDOMIZATION; VIRUS GENE; VIRUS MUTATION;

INFLUENZA A VIRUS;

EID: 84935001904     PISSN: 2314436X     EISSN: 23144378     Source Type: Journal    
DOI: 10.1155/2014/349139     Document Type: Article

References (25)

1. J. B. Plotkin and J. Dushoff, "Codon bias and frequencydependent selection on the hemagglutinin epitopes of influenza A virus, " Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 12, pp. 7152-7157, 2003.
2. G. J. D. Smith, D. Vijaykrishna, J. Bahl et al., "Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza a epidemic, " Nature, vol. 459, no. 7250, pp. 1122-1125, 2009.
3. M. R. Hilleman, "Realities and enigmas of human viral influenza: pathogenesis, epidemiology and control, " Vaccine, vol. 20, no. 25-26, pp. 3068-3087, 2002.
4. R. Grantham, C. Gautier, and M. Gouy, "Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type, " Nucleic Acids Research, vol. 8, no. 9, pp. 1893-1912, 1980.
5. G. M. Jenkins and E. C. Holmes, "The extent of codon usage bias in human RNA viruses and its evolutionary origin, " Virus Research, vol. 92, no. 1, pp. 1-7, 2003.
6. W. Gu, T. Zhou, J. Ma, X. Sun, and Z. Lu, "The relationship between synonymous codon usage and protein structure in Escherichia coli and Homo sapiens, " BioSystems, vol. 73, no. 2, pp. 89-97, 2004.
7. D. B. Levin and B. Whittome, "Codon usage in nucleopolyhedroviruses, " Journal of General Virology, vol. 81, part 9, pp. 2313- 2325, 2000.
8. T. Ikemura, "Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs, " Journal of Molecular Biology, vol. 158, no. 4, pp. 573-597, 1982.
9. P.M. Sharp, L. R. Emery, and K. Zeng, "Forces that influence the evolution of codon bias, " Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 365, no. 1544, pp. 1203-1212, 2010.
10. B.D.Greenbaum, A. J. Levine, G. Bhanot, and R. Rabadan, "Patterns of evolution and host gene mimicry in influenza and other RNAviruses, " PLoS Pathogens, vol. 4, no. 6, Article IDe1000079, 2008.
11. Z. P. Li, D. Ying, P. Li, F. Li, X. Bo, and S. Wang, "Analysis of synonymous codon usage bias in 09H1N1, " Virologica Sinica, vol. 25, no. 5, pp. 329-340, 2010.
12. T. Zhou, W. Gu, J.Ma, X. Sun, and Z. Lu, "Analysis of synonymous codon usage in H5N1 virus and other influenzaAviruses, " BioSystems, vol. 81, no. 1, pp. 77-86, 2005.
13. E.H.M. Wong, D. K. Smith, R. Rabadan, M. Peiris, and L. L. M. Poon, "Codon usage bias and the evolution of influenza A viruses. Codon Usage Biases of Influenza Virus, " BMC Evolutionary Biology, vol. 10, no. 1, article 253, 2010.
14. P. M. Sharp and W. Li, "The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications, "NucleicAcids Research, vol. 15, no. 3, pp. 1281-1295, 1987.
15. F. Wright, "The "effective number of codons" used in a gene, " Gene, vol. 87, no. 1, pp. 23-29, 1990.
16. J. M. Comeron and M. Aguadé, "An evaluation of measures of synonymous codon usage bias, " Journal of Molecular Evolution, vol. 47, no. 3, pp. 268-274, 1998.
17. J. A. Novembre, "Accounting for background nucleotide composition when measuring codon usage bias, " Molecular Biology and Evolution, vol. 19, no. 8, pp. 1390-1394, 2002.
18. L. E. Post and M. Nomura, "DNAsequences fromthe str operon of Escherichia coli, " Journal of Biological Chemistry, vol. 255, no. 10, pp. 4660-4666, 1980.
19. M. Gouy and C. Gautier, "Codon usage in bacteria: correlation with gene expressivity, " Nucleic Acids Research, vol. 10, no. 22, pp. 7055-7074, 1982.
20. J. Zhong, Y. Li, S. Zhao, S. Liu, and Z. Zhang, "Mutationpressure shapes codon usage in the GC-rich genome of foot-and-mouth disease virus, " Virus Genes, vol. 35, no. 3, pp. 767-776, 2007.
21. N.Goñi, A. Iriarte, V. Comas et al., "Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development, " Virology Journal, vol. 9, article 263, 2012.
22. S. Karlin, W. Doerfler, and L. R. Cardon, "Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses?" Journal of Virology, vol. 68, no. 5, pp. 2889-2897, 1994.
23. Y. Lavner and D. Kotlar, "Codon bias as a factor in regulating expression via translation rate in the human genome, " Gene, vol. 345, no. 1, pp. 127-138, 2005.
24. P. M. Sharp, M. Stenico, J. F. Peden, and A. T. Lloyd, "Codon usage: mtational bias, translational selection, or both?" Biochemical Society Transactions, vol. 21, no. 4, pp. 835-841, 1993.
25. A. J. Leigh Brown, "Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population, " Proceedings of the National Academy of Sciences of the United States of America, vol. 94, no. 5, pp. 1862-1865, 1997.